A comprehensive conformational analysis of tryptophan, its ionic and dimeric forms

• Published in: Journal of computational chemistry Vol. 35; no. 8; pp. 595 - 610
• Main Authors: Purushotham, Uppula, Sastry, G. Narahari
• Format: Journal Article
• Language: English
• Published: United States Blackwell Publishing Ltd 30.03.2014; Wiley Subscription Services, Inc
• Subjects: Amino acids; Chemistry; Conformational analysis; DFT; Dimerization; Hydrogen; Ions - chemistry; Molecular Conformation; Noncovalent interactions; PDB analysis; Preferences; Tryptophan - chemistry; Tryptophan dimer; DFT; Noncovalent interactions; PDB analysis; Conformational analysis; Tryptophan dimer
• ISSN: 0192-8651; 1096-987X; 1096-987X
• DOI: 10.1002/jcc.23482

Tryptophan is an essential amino acid, and understanding the conformational preferences of monomer and dimer is a subject of outstanding relevance in biological systems. An exhaustive first principles investigation of tryptophan (W) and its ionized counterparts cations (WC), anions (WA), and zwitterions (WZ) has been carried out. A comprehensive and systematic study of tryptophan dimer (WD) conformations resulted in about 62 distinct minima on the potential energy surface. The hydrogen bonds and a variety of noncovalent interactions such as OH‐π, NH‐π, CH‐π, CH‐O, and π‐π interactions stabilized different forms of tryptophan and its dimers. Over all in monomeric conformers which have NH‐O, hydrogen bonds showed higher stability than other conformers. A cursory analysis reveal that the most stable dimers stabilized by hydrogen bonding interactions while the less stable dimers showed aromatic side chain interactions. Protein Data Bank analysis of tryptophan dimers reveals that at a larger distance greater than 5 Å, T‐shaped orientations (CH‐π interactions) are more prevalent, while stacked orientations (π‐π interactions) are predominant at a smaller distance. © 2013 Wiley Periodicals, Inc. An exhaustive quantum mechanical analysis of tryptophan dimers and monomers is carried out. Protein Data Bank analysis of dimers reveals that stacked orientations are preferred at shorter centroid‐to‐centroid distances, while T‐shaped orientations are preferred at longer distances.